def test_local_fingerprinting(self):
"""Test the local fingerprint example"""
atoms = fcc111('Pd', size=(2, 2, 3), vacuum=10.0)
add_adsorbate(atoms, 'C', 1, 'fcc')
# -1 is the tag convention to identify bonded atoms
tags = atoms.get_tags()
tags[-1] = -1
atoms.set_tags(tags)
parameters = [
'atomic_number',
'atomic_radius',
'boiling_point',
'covalent_radius_cordero',
'evaporation_heat',
'fusion_heat',
'group_id',
'period',
]
operations = [
'bonding_convolution'
]
fp = Fingerprinter(atoms)
fingerprints = fp.get_fp(parameters, operations)
truth = np.array([276.0, 1.2467000000000001, 17406300.0,
1.0147, np.nan, np.nan, 140.0, 10.0])
np.testing.assert_allclose(fingerprints[0], truth)
def test_nonlocal_fingerprinting(self):
"""Test the non-local fingerprint example"""
atoms = bulk('Pd', cubic=True)
atoms[3].symbol = 'Pt'
slab = surface('Al', size=(2, 2, 3), a=3.8, vacuum=10)
images = [atoms, slab]
parameters = [
'atomic_number',
'atomic_radius',
'atomic_volume',
]
operations = [
'periodic_convolution',
['periodic_convolution', {'d': 1}]
]
fp = Fingerprinter(images)
fingerprints = fp.get_fp(parameters, operations)
truth = np.array([
[12432.0, 7.562800000000001, 320.44, 136896.0, 90.7488, 3844.8],
[2028.0, 24.53879999999999, 1200.0, 20280.0, 245.388, 12000.0]])
np.testing.assert_allclose(fingerprints, truth)
def test_custom_fingerprinting(self):
"""Test the custom fingerprint example"""
atoms = fcc111('Pd', size=(2, 2, 3), vacuum=10.0)
add_adsorbate(atoms, 'C', 1, 'fcc')
# -1 is the tag convention to identify bonded atoms
tags = atoms.get_tags()
tags[-1] = -1
atoms.set_tags(tags)
parameters = [
'atomic_number', 'dband_center_slab', 'dband_width_slab',
'dband_skewness_slab', 'dband_kurtosis_slab'
]
def example_operation(atoms, atoms_parameters, connectivity):
# This is a CatKit convention
bond_index = np.where(atoms.get_tags() == -1)[0]
return np.sum(connectivity[bond_index], axis=1)
operations = ['bonding_convolution', example_operation]
fp = Fingerprinter(atoms)
fingerprints = fp.get_fp(parameters, operations)
truth = np.array([
276.0, -1.570340288877117, 6.51684717398884, -81.36785228863994,
3651.4867376228817, 3.0
])
np.testing.assert_allclose(fingerprints[0], truth)
def test_local_fingerprinting(self):
"""Test the local fingerprint example"""
atoms = fcc111('Pd', size=(2, 2, 3), vacuum=10.0)
add_adsorbate(atoms, 'C', 1, 'fcc')
# -1 is the tag convention to identify bonded atoms
tags = atoms.get_tags()
tags[-1] = -1
atoms.set_tags(tags)
parameters = [
'atomic_number',
'atomic_radius',
'boiling_point',
'covalent_radius_cordero',
'evaporation_heat',
'fusion_heat',
'group_id',
'period',
]
operations = [
'bonding_convolution', 'layered_sum', 'local_ads_metal_fp'
]
fp = Fingerprinter(atoms)
fingerprints = fp.get_fp(parameters, operations)
truth = np.array([
276.0, 1.2467000000000001, 17406300.0, 1.0147, np.nan, np.nan,
140.0, 10.0, 6.0000e+00, 1.8400e+02, 1.8400e+02, 1.8400e+02,
9.1000e-01, 5.4800e+00, 5.4800e+00, 5.4800e+00, 5.1000e+03,
1.3652e+04, 1.3652e+04, 1.3652e+04, 7.3000e-01, 5.5600e+00,
5.5600e+00, 5.5600e+00, np.nan, 1.4896e+03, 1.4896e+03, 1.4896e+03,
np.nan, 6.8960e+01, 6.8960e+01, 6.8960e+01, 1.4000e+01, 4.0000e+01,
4.0000e+01, 4.0000e+01, 2.0000e+00, 2.0000e+01, 2.0000e+01,
2.0000e+01, 4.0000e+01, 4.6000e-01, -1.6870e+03, 6.6000e-01,
np.nan, np.nan, -4.0000e+00, 3.0000e+00
])
np.testing.assert_allclose(fingerprints[0], truth)
site=site,
site_type=site_type,
adsorbate=adsorbate,
reaction_energy=reactionenergy,
grepid=i)
fpd.image_entry(i)
fpd.fingerprint_entry(i, par[-1], reactionenergy)
fpd.metadata_entry(i, met_par[0], adsorbate)
fpd.metadata_entry(i, met_par[1], symbol)
fpd.metadata_entry(i, met_par[2], site)
fpd.metadata_entry(i, met_par[3], site_type)
fpd.metadata_entry(i, met_par[4], sb_symbol)
fp_nonlocal = Fingerprinter(slab)
fingerprints_nonlocal = fp_nonlocal.get_fp(parameters_list_nonlocal,
operation_list_nonlocal)
fp_local = Fingerprinter(structure)
fingerprints_local = fp_local.get_fp(parameters_list_local,
operation_list_local)
'''
try:
catlearn_fp = get_catlearn_fp(structure)
except AttributeError as e:
print('Got problem in catlearn.')
catlearn_fp = 'I\'m outta here.'
'''
if fingerprints_local == 'I\'m outta here.':
print('Got problem in local.')
continue